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Delineation of Key Regulatory Elements Identifies Points Of DELINEATION OF KEY REGULATORY ELEMENTS IDENTIFIES POINTS OF VULNERABILITY IN THE MITOGEN-ACTIVATED SIGNALING NETWORK SUPPLEMENTARY MATERIALS List of contents Supplementary Figures with legends 1. Figure S1: Distribution of primary siRNA screen data, and standardization of assay procedure. 2. Figure S2: Scatter plot of screen data. 3. Figure S3: Functional relevance of the identified targets and Calculation of residence time from PDT and cell cycle distribution. 4. Figure S4: FACS profiles for ABL1 and AKT1. Table for data in Figure 5B. 5. Figure S5: Venn diagram showing the results of the comparative analysis of other screen results 6. Figure S6: Dose response profiles for the AKT1 + ABL1 inhibitor combination for CH1, list of the 14 cell lines and their description, effect of ABL1+AKT1 inhibitor combination on increase in apoptotic cells and G1 arrest in 14 cell lines, effects of CHEK1 inhibitor on combination C1,C2 on 4 cell lines. Supplementary Tables 1. Table S1: siRNA screen results for targeted kinases and phosphatases. 2. Table S2: Gene expression status of the validated hits. 3. Table S3: Role played by identified RNAi hits in regulation of cell cycle, the effect on PDTs along with phase-specific RTs. 4. Table S4: List of molecules classified as cell cycle targets. 5. Table S5: High confidence network used for graph theory analysis. 6. Table S6: Occurrences of nodes in shortest path networks. 7. Table S7: Network file used as SNAVI background. 8. Table S8: Classification of nodes present in modules according to specificity. Legends for tables Supplementary Experimental Procedures References Figure S1 A 450 400 G1 S 350 G2 300 250 200 150 100 50 Distribution of molecules Distribution 0 -6-4-20246 Z-score 350 200 400 G1 S 300 G2 150 300 250 200 100 200 150 100 50 100 Distribution of molecules 50 0 0 0 -4 -2 0 2 4 -4-20246 -4-20246 Z-score B PLK1 GAPDH PLCg BTK PLCg CDC2A PLCg CHEK1 PLCg MET Distribution profiles of complete primary screen and western blots showing knockdown efficiency. Plotted in panel A are the mean z-scores of the replicates for the entire screen with siRNA targeting kinases and phosphatases. The graph shows the distribution of the data points for all the molecules targeted. The normal nature of the distribution curve, with minimal skewness, confirms the robustness of the screen. Panel B shows the effect of siRNA knockdown of 5 targets at 96 hours post transfection. siRNAs targeting BTK and PLK1 were used for screen standardizations. The reductions in protein levels were monitored at 24, 36, 48, 72 and 96 hours post transfection. At each of these time points cells were harvested, lysed and the levels of the respective proteins in the cytoplasm detected by Western blot analysis. Silencing of select proteins, which includes 3 validated screen hits (CHEK1, MET and CDC2A) at 96 hours after transfection is shown here. Here either GAPDH (for PLK1), or PLCg (for the remaining molecules) were also probed in parallel to serve as the loading control. The antibodies were obtained from Cell Signaling Technology. (Also refer Figure 1). Figure S2 8.00 Replicate 1 Replicate 2 G1 6.00 Chka Chka 4.00 2.00 0.00 -50 50 150 250 350 450 550 650 750 850 950 1050 1150 1250 1350 1450 1550 1650 1750 1850 1950 2050 2150 2250 -2.00 -4.00 -6.00 -8.00 6.00 Replicate 1 Replicate 2 S 4.00 Prkar1a Prkar1a 2.00 0.00 -50 50 150 250 350 450 550 650 750 850 950 1050 1150 1250 1350 1450 1550 1650 1750 1850 1950 2050 2150 2250 Z-score -2.00 -4.00 -6.00 -8.00 8.00 Replicate 1 Replicate 2 6.00 G2 4.00 2.00 0.00 -50 50 150 250 350 450 550 650 750 850 950 1050 1150 1250 1350 1450 1550 1650 1750 1850 1950 2050 2150 2250 -2.00 -4.00 MET MET -6.00 -8.00 -10.00 Molecules Scatter plot of z-scores to verify reproducibility of the primary siRNA screen Shown are the scatter plots for the two individual replicate z-scores for the three different phases. (Refer Figure 1) Figure S3 A B 100 Adenocarcinoma Gastric adenocarcinoma Lung adenocarcinoma Adenoma Adrenocortical adenoma Follicular adenoma Anaplastic astrocytoma 90 Anaplastic oligodendroma Astrocytoma Biliary tract cancer Bladder cancer Brain tumour Breast cancer 80 Breast carcinoma Cancer Lung cancer Carcinoma Ductal carcinoma Embryonal carcinoma Neuroendocrine carcinoma 70 Non small cell lung carcinoma Squomous cell carcinoma Cervical cancer/carcinoma Cholangiocarcinoma Chondrosarcoma Colon cancer Colon carcinoma 60 Colorectal cancer Colorectal carcinoma/tumor Endometrial cancer/carcinoma Epithelial tumour Esophagial carcinoma Gastric cancer/carcinoma Glioblastoma 50 Glioma Hepatocellular carcinoma Leukemia –log (P-value) Lymphocytic leukemia T cell leukemia Lung carcinoma 40 Lymphoma B cell lymphoma Non hodgkins lymphoma T cell lymphoma Mammary tumour Melanoma Metastasis 30 Metastatic melanoma Multiple tumors Myeloid leukemia Oral cancer Osteosarcoma Ovarian cancer Ovarian carcinoma 20 Pancreatic cancer Pancreatic carcinoma Primary tumor Promyelocytic leukemia Prostrate cancer Prostrate carcinoma 10 Retinoblastoma Rhabdosarcoma Sarcoma Skin cancer Solid tumors Thyroid cancer Tumors 0 Functional relevance of the identified targets and Calculation of residence time from PDT and cell cycle distribution Panel A depicts the gene-disease relationship score (indicated by the color bar) of our hits with various forms of cancer. These scores were obtained as –log (P-value) from Novoseek gene-disease database. Panel B shows the schematic to explain the method followed to calculate RT for CH1 cells after targeted siRNA mediated perturbation of screen hits. The approach is illustrated by taking the case of PLK1 as a typical example. (Refer Figure 1C and 1D) Figure S4 A # Cells B Panel A shows the histograms obtained from a cell cycle analysis of CH1 cells at 48 hours post treatment with 0.5 x IC50 of ABL1 and AKT1 inhibitor (i.e Imatinib mesylate and LY294002). The respective RTs of the G1, S and G2 phases are indicated. (Figure 5A). Panel B lists the siRNA sequences employed for silencing of the high stress and betweeness targets shown in Figure 5B. Figure S5 A B C D E Panel A shows the Venn diagram comparing the overlap of IMP nodes identified from the three different screens. Panel B shows the Venn diagram comparing the overlap of nodes from the IMP node networks of the three different screens. Panel C is the comparison between IMP nodes identified from three sets of randomly sampled source-target pairs. A very poor overlap can be observed here. Panel D is the comparison between IMP nodes identified from three sets of randomly sampled sources but retaining the target nodes to assess target biasness in IMP nodes selection. Again a very poor overlap can be observed here. Panel E is the comparison between IMP nodes identified from three sets of randomly sampled sources and the IMP nodes identified from our study in CH1. A very poor overlap can be observed here when compared to the overlap observed between U2OS and HeLa cells. Figure S6 A B G1 population Dead cells 70 70 60 AAKT1 60 AABL1 AAKT1+ABL1 50 50 40 40 30 20 % % Apoptotic cells 30 10 20 0 0.01 0.1 1 10 0.01 0.1 1 10 Dose (x IC50) C % % Apoptotic cells DE G1 % cells % G1 Δ % % Apoptotic cells Panel A depicts the dose-response profile for increase in G1 population, and increase in apoptotic cells in CH1 cells treated with pharmacological inhibitors of ABL1, AKT1 and the combination of the respective doses. Doses for each inhibitor used were in multiples of their corresponding IC50 values as indicated. Values (mean ± S.D. of three experiments) are expressed as the percent of cells obtained at 48h post treatment. (Also refer Figure 5). Panel B lists and describes all the human cell lines used in this study. In Panel C, the effect of inhibition of ABL1, AKT1 and their combination (at concentrations corresponding to 5 times their respective IC50 values) on inducing apoptosis of fourteen different human cancer cell lines is shown. Here, the cells were treated with a single addition of the inhibitor or inhibitor combination, and the frequency of apoptotic cells was determined 48h later. In all cases, results are the mean (± S.D.) of three experiments. In Panel D, cells of the indicated cancer cell lines were treated with inhibitors against either the indicated kinase, or the kinase combinations and the consequent effect on cellular apoptosis was determined 48 hours later. The concentration of the relevant inhibitor employed was five-fold greater than its corresponding IC50 value in all cases and results are the mean (± S.D.) of three experiments. The protocol followed was similar to panel C. As is evident, with the exception of Jurkat cells, apoptosis resulted from the dominant effects of CHEK1 inhibition in all cases (Refer Figure 7). Panel E depicts the increase in G1 population observed in the fourteen different human cancer cell lines following treatment with inhibitors of both ABL1 and AKT1 (at concentration corresponding to their IC50 values). Values (mean ± S.D., n=3) are those obtained at 24 h post-treatment and are expressed as increase in the percent of cells in the G1 phase, relative to that in the absence of any inhibitor (i.e. vehicle only). Table S3 Classification of hits based on RT affecting the cell cycle phases Observed Population Phenotype Total No. GO Involved Doubling (Based on of GO Cell Cycle or time increase in RT) Pubmed IDs for Cell Cycle role known Role in cell proliferation terms Proliferation Ratio Residence Time (Hours)(Hours) Std.
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